› 4mej

X-ray diffraction
2.1Å resolution

Crystal structure of Lactobacillus helveticus purine deoxyribosyl transferase (PDT) with the tricyclic purine 8,9-dihydro-9-oxoimidazo[2,1-b]purine (N2,3-ethenoguanine)

Released:
DOI: 10.2210/pdb4mej/pdb
PDB entry 4mej coloured by chain, front view.
PDB entry 4mej coloured by chain, side view.
PDB entry 4mej coloured by chain, top view.
Source organism: Lactobacillus helveticus H10
Primary publication:
Glycosylation of a tricyclic purine analog at alternative sites by nucleoside 2 -deoxyribosyltransferases
Ye W, Paul D, Gao L, Seckute J, Sangaiah R, Karupiah J, Zhang Z, Kaminski AP, Ealick SE, Gold A, Ball LM
PLoS ONE (2014)

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-123263 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nucleoside deoxyribosyltransferase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 167 amino acids
Theoretical weight: 18.73 KDa
Source organism: Lactobacillus helveticus H10
Expression system: Escherichia coli
UniProt:
  • Canonical: F0NW64 (Residues: 1-167; Coverage: 100%)
Gene name: LBHH_1694
Sequence domains: Nucleoside 2-deoxyribosyltransferase
Structure domains: Rossmann fold

Ligands and Environments

2 bound ligands:
Ligand SO4 2 x SO4
Ligand 28Y 3 x 28Y
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P43212
Unit cell:
a: 79.695Å b: 79.695Å c: 186.697Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.197 0.195 0.229
Expression system: Escherichia coli

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